PDB Short entry for 4SOD HEADER OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR) 14-JAN-93 4SOD TITLE RATIONAL DESIGN AND EXPRESSION OF A HEPARIN-TARGETED HUMAN TITLE 2 SUPEROXIDE DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER,ZINC SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS KEYWDS OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR) EXPDTA THEORETICAL MODEL AUTHOR L.A.KUHN,C.L.FISHER,J.A.TAINER REVDAT 1 30-APR-94 4SOD 0 JRNL AUTH M.BOISSINOT,L.A.KUHN,P.LEE,C.L.FISHER,Y.WANG, JRNL AUTH 2 R.A.HALLEWELL,J.A.TAINER JRNL TITL RATIONAL DESIGN AND EXPRESSION OF A JRNL TITL 2 HEPARIN-TARGETED HUMAN SUPEROXIDE DISMUTASE. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 190 250 1993 JRNL REFN ASTM BBRCA9 US ISSN 0006-291X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.E.PARGE,R.A.HALLEWELL,J.A.TAINER REMARK 1 TITL ATOMIC STRUCTURES OF WILD-TYPE AND THERMOSTABLE REMARK 1 TITL 2 MUTANT RECOMBINANT HUMAN CU,ZN SUPEROXIDE DISMUTASE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6109 1992 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.A.KUHN,J.H.GRIFFIN,C.L.FISHER,J.S.GREENGARD, REMARK 1 AUTH 2 B.N.BOUMA,F.ESPANA,J.A.TAINER REMARK 1 TITL ELUCIDATING THE STRUCTURAL CHEMISTRY OF REMARK 1 TITL 2 GLYCOSAMINOGLYCAN RECOGNITION BY PROTEIN C REMARK 1 TITL 3 INHIBITOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 87 8506 1990 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4SOD COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 RESIDUES 1 - 153 CORRESPOND TO THE THERMOSTABLE MUTANT REMARK 5 HUMAN CU,ZN SOD STRUCTURE WITH CYS 6 -> ALA AND CYS 111 -> REMARK 5 SER (REF. 1 AND PDB ENTRY 1SOS). THE HEPARIN-BINDING REMARK 5 PEPTIDE IS MODELLED AS A HELIX BASED UPON REF. 2 AND PDB REMARK 5 ENTRY 1PAI. THE FUSION PROTEIN STRUCTURE IS SUBSTANTIALLY REMARK 5 SIMILAR TO THAT OF HUMAN CU,ZN SOD ("HSOD"), WITH THE ADDED REMARK 5 GLY-PRO-GLY-A+ HELIX PEPTIDE FORMING AN EXTENSION THAT REMARK 5 PACKS AGAINST THE LOOPS AT ONE END OF THE BETA-BARREL. REMARK 5 SEQUERY, A PROGRAM THAT SEARCHES THE PROTEIN DATA BANK FOR REMARK 5 SEQUENCE PATTERNS (L. A. KUHN, M. E. PIQUE, M. A. SIANI, REMARK 5 E. D. GETZOFF, AND J. A.TAINER), WAS USED TO CONFIRM THAT REMARK 5 THE GLY-PRO-GLY LINKER HAS A CONFORMATION THAT ENCOURAGES REMARK 5 THE HELIX ATTACHED TO EACH HSOD SUBUNIT TO PACK IN THIS REMARK 5 ORIENTATION. THIS FORMS A TWO-HELIX HEPARIN-BINDING MOTIF REMARK 5 (REF. 2) IN THE DIMERIC PROTEIN. THE MODELLED STRUCTURE REMARK 5 GUIDED THE DESIGN OF A FUSION PROTEIN (HSOD-GLY-PRO-GLY-A+) REMARK 5 MADE BY RECOMBINANT DNA TECHNIQUES. THIS PROTEIN WAS REMARK 5 EXPRESSED IN ESCHERICHIA COLI AND SHOWN TO HAVE NORMAL SOD REMARK 5 ACTIVITY AND INCREASED RETENTION ON A HEPARIN AFFINITY REMARK 5 COLUMN RELATIVE TO WILD-TYPE HSOD. SEE JRNL ENTRY ABOVE REMARK 5 FOR DETAILS ON THE DESIGN, CONSTRUCTION, AND TESTING. REMARK 6 REMARK 6 IN REGARD TO THE NON-TRANS PEPTIDES LISTED BELOW, IN ALL REMARK 6 CASES THE O-C-N-H BONDS ARE PLANAR BUT THE CA-C-N-CA BONDS REMARK 6 ARE NONPLANAR AND THERE IS A DISTORTION IN THE N-H BOND. REMARK 6 THIS MAY BE DUE TO ENERGY MINIZATION PROBLEMS, OR THE REMARK 6 PROCESS OF FORMING THE BOND BETWEEN RESIDUE 153 (THE REMARK 6 NATURAL C-TERMINUS OF HSOD) AND RESIDUE 154 (THE NATURAL REMARK 6 N-TERMINUS OF THE HEPARIN BINDING HELIX). REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ARG A 158 135.02 69.26 REMARK 500 1 HIS A 159 -61.93 69.15 REMARK 500 2 ARG A 158 135.05 69.20 REMARK 500 2 HIS A 159 -61.90 69.14 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 25 ASN A 26 1 149.83 REMARK 500 ALA A 152 GLN A 153 1 -148.04 REMARK 500 SER A 25 ASN A 26 2 149.86 REMARK 500 ALA A 152 GLN A 153 2 -148.08 DBREF 4SOD A 1 171 GB 1045507 AAA80237 1 171 SEQRES 1 A 172 ACE ALA THR LYS ALA VAL ALA VAL LEU LYS GLY ASP GLY SEQRES 2 A 172 PRO VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER SEQRES 3 A 172 ASN GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU SEQRES 4 A 172 THR GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY SEQRES 5 A 172 ASP ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE SEQRES 6 A 172 ASN PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU SEQRES 7 A 172 GLU ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP SEQRES 8 A 172 LYS ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL SEQRES 9 A 172 ILE SER LEU SER GLY ASP HIS SER ILE ILE GLY ARG THR SEQRES 10 A 172 LEU VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY SEQRES 11 A 172 GLY ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER SEQRES 12 A 172 ARG LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN GLY PRO SEQRES 13 A 172 GLY HIS ARG HIS HIS PRO ARG GLU MET LYS LYS ARG VAL SEQRES 14 A 172 GLU ASP LEU FTNOTE 1 SER 25 - ASN 26 MODEL 1 OMEGA =149.83 PEPTIDE BOND FTNOTE 1 DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 2 ALA 152 - GLN 153 MODEL 1 OMEGA =211.96 PEPTIDE BOND FTNOTE 2 DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 3 SER 25 - ASN 26 MODEL 2 OMEGA =149.86 PEPTIDE BOND FTNOTE 3 DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 4 ALA 152 - GLN 153 MODEL 2 OMEGA =211.92 PEPTIDE BOND FTNOTE 4 DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION HET ACE A 0 6 HETNAM ACE ACETYL GROUP FORMUL 1 ACE C2 H4 O HELIX 1 1 ASN A 131 GLY A 138 1 8 HELIX 2 2 HIS A 159 GLU A 169 1 11 SHEET 1 A 4 LYS A 3 LYS A 9 0 SHEET 2 A 4 GLN A 15 GLN A 22 -1 N GLY A 16 O LEU A 8 SHEET 3 A 4 VAL A 29 LYS A 36 -1 N LYS A 30 O GLU A 21 SHEET 4 A 4 VAL A 94 ASP A 101 -1 N ALA A 95 O ILE A 35 SHEET 1 B 4 ASP A 83 ALA A 89 0 SHEET 2 B 4 GLY A 41 HIS A 48 -1 O GLY A 41 N ALA A 89 SHEET 3 B 4 THR A 116 HIS A 120 -1 O THR A 116 N HIS A 48 SHEET 4 B 4 ARG A 143 VAL A 148 -1 N LEU A 144 O VAL A 119 SSBOND 1 CYS A 57 CYS A 146 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000